Most microbiology work in marine subsurface sediments has been focused in the upper 100-200 meters of sediment, partially because the switchover from Advanced Piston Coring (APC) to Extended Core Barrel (XCB) coring generally occurs around this depth, which leads to large increases in drilling-induced contamination. Molecular studies in deeper samples may be greatly hindered by the potential interferences from these contaminating microbes. This project provides an extensive next-generation sequencing based study coupling the analysis of microbial community composition to great depth in the Costa Rica Margin subseafloor to the analysis of the drilling fluid used in the process of obtaining those samples. In nearly all samples examined, the influence of drilling-fluid in molecular analysis of the sediment samples was very low, even in several samples taken with XCB coring. One sample from 496 mbsf was shown to contain a high proportion of sequences potentially originated from drilling fluid, however, which suggests that it is still important to routinely include comparison to drilling fluid as a control in molecular analyses. This study also provides a first and extensive look at the microbial community composition of the Costa Rica Margin subseafloor from 2 sites on the upper plate of the erosive subduction zone between the Cocos and Caribbean plates. These 2 sites, while in close proximity and sharing many physical and chemical properties, showed distinction in terms of the relative abundances of microbial groups, particularly in the proportion of archaea to bacteria. Additionally, correlations assessed between microbial taxa and geochemistry variables suggest directions for future research into the metabolic capabilities of some uncharacterized subseafloor microbial lineages.